Variant report

Variant	rs2460647
Chromosome Location	chr15:56509908-56509909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56498392..56501238-chr15:56507855..56509963,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11629483	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631191	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900678	0.96[CEU][hapmap];0.91[MEX][hapmap]
rs12905782	0.92[CEU][hapmap]
rs12905899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911094	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911427	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914640	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1442640	0.81[EUR][1000 genomes]
rs1549452	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs17819438	1.00[CEU][hapmap]
rs1829542	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249090	0.92[CEU][hapmap];0.91[MEX][hapmap]
rs2303441	1.00[CEU][hapmap]
rs2414464	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460648	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682044	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682046	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682049	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682053	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2682054	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2682059	1.00[CEU][hapmap]
rs2713923	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713926	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713933	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2713935	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2713936	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2713938	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2718915	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2718934	1.00[CEU][hapmap]
rs2718941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725854	0.96[CEU][hapmap]
rs2725870	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap]
rs34044869	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34144128	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34224072	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34386737	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34756325	0.84[ASN][1000 genomes]
rs35082998	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35749329	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35972806	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4310791	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774232	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774847	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774848	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59432349	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044110	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044111	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493835	0.84[ASN][1000 genomes]
rs6493856	0.96[CEU][hapmap]
rs7165270	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7168319	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174823	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175745	0.80[EUR][1000 genomes]
rs7176107	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs7496025	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8024031	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028353	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8029114	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8033653	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9672886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672928	0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2460647	RFX7	cis	Adipose Subcutaneous	GTEx
rs2460647	FLJ12994	cis	multi-tissue	Pritchard
rs2460647	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56453600-56515000	Weak transcription	NHLF	lung
2	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
3	chr15:56466000-56514200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:56467000-56511600	Weak transcription	Fetal Intestine Small	intestine
5	chr15:56480200-56515400	Weak transcription	Hela-S3	cervix
6	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:56493200-56515400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:56496600-56515200	Weak transcription	Left Ventricle	heart
9	chr15:56498400-56514400	Weak transcription	NHEK	skin
10	chr15:56498400-56515200	Weak transcription	HUVEC	blood vessel
11	chr15:56500600-56513000	Weak transcription	HMEC	breast
12	chr15:56500600-56515200	Weak transcription	Ovary	ovary
13	chr15:56500800-56514400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:56500800-56515200	Weak transcription	Thymus	Thymus
15	chr15:56501600-56511800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:56502400-56514600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:56504200-56515200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:56504600-56511800	Weak transcription	Fetal Kidney	kidney
19	chr15:56504800-56510800	Weak transcription	HSMM	muscle
20	chr15:56504800-56511600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:56504800-56511800	Weak transcription	K562	blood
22	chr15:56504800-56515200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:56505000-56515200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:56505600-56513600	Weak transcription	Brain Anterior Caudate	brain
25	chr15:56505600-56514400	Weak transcription	HepG2	liver
26	chr15:56505800-56511600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:56505800-56514800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:56506000-56514200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:56506200-56510600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:56506400-56510600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:56506400-56511600	Weak transcription	Fetal Lung	lung
32	chr15:56506400-56514400	Weak transcription	Dnd41	blood
33	chr15:56507200-56510200	Enhancers	NH-A	brain
34	chr15:56508000-56534400	Weak transcription	Fetal Heart	heart
35	chr15:56508200-56511600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:56508200-56512800	Weak transcription	Primary T cells from cord blood	blood
37	chr15:56508200-56515400	Weak transcription	Fetal Thymus	thymus
38	chr15:56508200-56524000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:56508400-56510000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:56508400-56510000	Weak transcription	Primary B cells from cord blood	blood
41	chr15:56508400-56510600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:56508400-56513000	Weak transcription	A549	lung
43	chr15:56508400-56514400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:56508400-56515200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:56508400-56523000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:56508800-56510800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:56508800-56511800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:56508800-56514200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:56508800-56514600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:56508800-56515000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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